Contacts of the helix formed by residues 203 - 212 (chain A) in PDB entry 3NBV
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 203 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A PHE* 4.4 0.3 - - - +
202A GLN* 1.3 80.3 - - - +
204A ALA* 1.3 64.7 + - - +
205A GLU* 3.2 18.5 + - - +
206A GLU* 3.2 24.5 + - - +
207A ALA* 3.0 24.6 + - - +
225A TRP* 3.5 16.4 - - - -
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Residues in contact with ALA 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A SER* 1.3 74.0 - - - +
205A GLU* 1.3 58.2 + - - +
207A ALA* 3.4 1.7 + - - +
208A LEU* 3.0 35.0 + - - +
223A CYS* 3.7 29.1 - - + +
225A TRP* 3.4 30.3 - - + -
230A ALA* 5.1 0.4 - - - -
231A ASP* 3.8 22.0 - - + +
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Residues in contact with GLU 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A SER* 3.2 16.4 + - - +
204A ALA* 1.3 79.1 - - - +
206A GLU* 1.3 77.0 + - - +
208A LEU* 3.4 2.8 + - - +
209A ARG* 3.1 32.6 + - + +
231A ASP* 3.9 10.6 + - - +
239A LEU* 3.6 34.4 - - + +
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Residues in contact with GLU 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A GLY 4.3 5.8 - - - +
201A PHE* 3.5 27.1 - - + -
202A GLN* 3.1 30.5 + - - +
203A SER* 3.2 19.3 + - - +
205A GLU* 1.3 86.9 - - - +
207A ALA* 1.3 57.6 + - - +
209A ARG* 3.4 5.6 + - + +
210A GLY 2.9 24.3 + - - -
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Residues in contact with ALA 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A VAL* 5.7 0.4 - - + -
196A ALA* 3.6 28.5 - - + -
201A PHE* 3.7 17.2 - - + +
203A SER 3.0 18.7 + - - +
204A ALA 3.7 5.2 - - - +
206A GLU* 1.3 77.7 - - - +
208A LEU* 1.3 57.4 + - - +
210A GLY 3.3 0.5 + - - -
211A LEU* 2.9 42.4 + - + +
223A CYS* 4.4 11.7 - - + -
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Residues in contact with LEU 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A VAL* 5.2 0.9 - - + -
204A ALA 3.0 17.4 + - - +
205A GLU 3.7 4.0 - - - +
206A GLU 3.3 0.4 - - - -
207A ALA* 1.3 74.1 - - - +
209A ARG* 1.3 65.9 + - - +
212A TYR* 3.0 29.6 + - - +
221A LEU* 3.5 45.3 - - + +
223A CYS* 4.1 17.0 - - + +
231A ASP* 3.4 34.1 - - + +
232A ALA 3.6 17.5 - - - +
233A LEU* 3.7 14.0 - - + +
239A LEU* 3.7 17.0 - - + -
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Residues in contact with ARG 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A GLU* 3.1 24.2 + - - +
206A GLU* 3.8 4.9 - - + +
208A LEU* 1.3 77.0 - - + +
210A GLY* 1.3 63.0 + - - +
211A LEU 3.3 0.9 + - - -
212A TYR* 3.9 6.6 + - - +
213A GLY 4.9 1.9 + - - -
233A LEU* 3.9 23.7 - - - +
237A GLY* 3.1 31.3 + - - -
239A LEU* 3.9 28.8 - - + +
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Residues in contact with GLY 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A PHE* 3.6 26.3 - - - -
206A GLU 2.9 12.4 + - - -
207A ALA 3.7 0.9 - - - -
208A LEU 3.3 0.2 - - - -
209A ARG* 1.3 78.7 - - - +
211A LEU* 1.3 65.3 + - - +
213A GLY* 4.9 2.0 + - - -
214A ARG* 5.3 2.4 + - - +
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Residues in contact with LEU 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A PHE* 4.0 26.3 - - + -
191A VAL* 4.2 21.8 - - + -
196A ALA* 5.2 3.6 - - - -
199A LEU* 3.6 30.3 - - + -
201A PHE* 3.9 16.8 - - + -
207A ALA* 2.9 26.1 + - + +
210A GLY* 1.3 79.7 - - - +
212A TYR* 1.3 68.3 + - - +
213A GLY 3.0 4.0 - - - -
214A ARG* 3.0 43.5 + - - +
215A VAL* 4.1 3.6 + - - +
221A LEU* 3.9 13.1 - - + +
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Residues in contact with TYR 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A LEU 3.0 17.7 + - - +
209A ARG 3.9 5.0 + - - +
210A GLY 3.7 0.6 - - - -
211A LEU* 1.3 78.9 - - - +
213A GLY* 1.3 63.4 + - - +
215A VAL* 3.0 34.3 - - + +
216A ARG 5.8 0.7 - - - -
217A LYS* 6.4 0.9 - - - -
218A GLY 4.5 3.1 + - - -
219A ALA 2.7 28.3 + - - -
221A LEU* 3.8 16.1 - - + +
233A LEU* 3.2 45.5 - - + -
234A GLY 3.7 11.2 - - - -
235A PRO* 3.1 25.5 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il